Entity properties are stored inside a 3d VueEntity as attributes and managed through the VueEntityAttributes interface
The list of out of the box attributes is defined in the interface itself
The ones you make reference are ATTRIB_VISIBILITY and ATTRIB_COLOR
they take a Boolean and Color respectively

Usually, getting a hold of a 3D entity is done through the selection (ie user clicks and selects a body), and it is acheived through the VueBean VueController Vue3DController
and selector interfaces
To get a hold on the selected entities you invoke something like
VueEntity[] ents = vuebean.getController().get3DController().getSelector().get();

Then modifying the attributes through the attrib interface. Attributes are divided into model and user defined (overidable) attributes.
In your particular case, you need to modify the overridable attibute, a simple way to access those is
to get an attibute value
VueEntityAttributes vea = entity.getEntityAttributes();
Boolean vis = (Boolean)vea.getEffectiveAttribute(VueEntityAttributes.ATTRIB_VISIBILITY);
to set the value
VueEntityAttributes vea = entity.getEntityAttributes();
vea.setUserAttribute(VueEntityAttributes.ATTRIB_VISIBILITY, Boolean.TRUE);